BN1809 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.9449e-07 1.0756e-03
Layer 2 3.4113e-05 1.7300e-02
Layer 4 3.4388e-03 4.8530e-02
Layer 5 4.8875e-03 2.8121e-02
Layer 6 6.9627e-03 2.0964e-02
Layer 1 5.2887e-02 2.8468e-01
WM 2.9921e-01 2.4056e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
UQCRH Expression Distribution
Gene Specificity Score (GSS)
UQCRH GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
UQCRH Layer 3 2.3496 0.6476
GHITM Layer 3 2.2773 0.6352
NDRG4 Layer 3 2.5664 0.6330
WBP2 Layer 3 2.4238 0.6326
GRIN1 Layer 3 2.4844 0.6276
RCAN2 Layer 3 2.3594 0.6252
C9orf16 Layer 3 2.5273 0.6239
ATP1B1 Layer 3 2.4082 0.6220
ATP5F1B Layer 3 2.4785 0.6211
NSF Layer 3 2.4395 0.6206
SCN1B Layer 3 3.0781 0.6198
NCS1 Layer 3 2.4570 0.6188
CAMTA1 Layer 3 2.4570 0.6187
INA Layer 3 2.5898 0.6183
CABP1 Layer 3 2.6367 0.6178
ATP5F1D Layer 3 2.3281 0.6170
OLIG1 Layer 3 2.2520 0.6164
CDIP1 Layer 3 2.3652 0.6153
DNM1 Layer 3 2.4609 0.6140
BEX3 Layer 3 2.4180 0.6135
PPP2R1A Layer 3 2.4512 0.6132
TLE5 Layer 3 2.3027 0.6130
PIN1 Layer 3 2.4609 0.6115
NDFIP1 Layer 3 2.3281 0.6112
NEFH Layer 3 3.1660 0.6110
LDHB Layer 3 2.5059 0.6088
APBB1 Layer 3 2.3125 0.6087
CCK Layer 3 2.4727 0.6080
ANXA6 Layer 3 2.4180 0.6074
NDUFA4 Layer 3 2.3965 0.6069
FAIM2 Layer 3 2.4297 0.6067
EEF1A2 Layer 3 2.4336 0.6066
NEFM Layer 3 3.2500 0.6062
GDI1 Layer 3 2.3418 0.6057
NAPA Layer 3 2.4102 0.6054
QDPR Layer 3 2.5146 0.6040
PRKAR1B Layer 3 2.4941 0.6031
DYNLL2 Layer 3 2.3242 0.6028
PRDX2 Layer 3 2.5332 0.6023
MORF4L1 Layer 3 2.3867 0.6017
VSTM2A Layer 3 2.2070 0.6013
ATP1A3 Layer 3 2.4023 0.6012
CHCHD10 Layer 3 2.3994 0.6011
INPP5F Layer 3 2.3027 0.6009
CPLX1 Layer 3 2.5566 0.6006
SULT4A1 Layer 3 2.2852 0.6004
SYT2 Layer 3 2.6484 0.6000
RPH3A Layer 3 2.4590 0.5998
CAMK2G Layer 3 2.4570 0.5997
TPI1 Layer 3 2.3838 0.5995

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1809
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1809_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1809/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1809/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1809/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1809/report/PD/BN1809_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1809/report/PD/BN1809_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 07:28:34
  • Number of Processes: 10
  • Spending Time: 0h 2m